Re: CA CL CA angle?

From: Brian Bennion (
Date: Tue Nov 01 2005 - 12:57:43 CST


In your bond assignments in the top.inp file there is a place where you
have listed CL bonding to two other C atoms. Or something of that flavor.
Psfgen then reads the bond info and by default finds angles and dihedrals
for those bonds and puts those entries in the .psf file.

I would check the psf file for two bond entries for the Cl index number.


Its amazing that namd ever becaming popular without a email list hmmm...

On Tue, 1 Nov 2005, Richard Wood wrote:

> Hi all,
> I have a chlorinated tyrosine residue that I have
> created a topology for (I asked for help and no one
> responded, so I proceeded on my own), and I am now
> trying to run an energy minimization on my molecule.
> Of course, it asks for parameters, first for vdW
> parameters for Cl, then for a C-Cl bond, then for a
> C-C-Cl angle. All of these I put in my parameter
> file. Then, when I run my calculation, it asks for
> the parameters for a CA CL CA angle, of which there is
> no such thing! (Or maybe there is?) What do i do?
> Richard
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  Brian Bennion, Ph.D.
  Bioscience Directorate
  Lawrence Livermore National Laboratory
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